Dear all,
I am interested in using the GBS method and then perform SNP detection on Illumina reads.
However, I am not sure about which would be the appropriate software to preform this task on:
i) a de novo species
ii) using a draft reference genome with multiple scaffolds
What about using VarScan for the first case and TASR for the second?
Does anyone has any experience with these....I also wonder if STACKs will perform well on these data...
Thanks in advance,
Fernando
I am interested in using the GBS method and then perform SNP detection on Illumina reads.
However, I am not sure about which would be the appropriate software to preform this task on:
i) a de novo species
ii) using a draft reference genome with multiple scaffolds
What about using VarScan for the first case and TASR for the second?
Does anyone has any experience with these....I also wonder if STACKs will perform well on these data...
Thanks in advance,
Fernando
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